| plot_precision_recall |
2 |
- plots/precision-recall/simulated-bwa.INS.svg
- plots/precision-recall/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| svg2pdf |
14 |
- plots/precision-recall/simulated-bwa.INS.pdf
- plots/precision-recall/simulated-bwa.DEL.pdf
- plots/fdr-control/simulated-bwa.INS.pdf
- plots/fdr-control/simulated-bwa.DEL.pdf
- plots/allelefreqs/simulated-bwa.INS.pdf
- plots/allelefreqs/simulated-bwa.DEL.pdf
- plots/score-dist/simulated-bwa.INS.pdf
- plots/score-dist/simulated-bwa.DEL.pdf
- plots/allelefreq-recall/simulated-bwa.INS.pdf
- plots/allelefreq-recall/simulated-bwa.DEL.pdf
- plots/allelefreq-scatter/simulated-bwa.INS.pdf
- plots/allelefreq-scatter/simulated-bwa.DEL.pdf
- plots/concordance/colo1.INS.concordance.pdf
- plots/concordance/colo1.DEL.concordance.pdf
|
|
|
| plot_fdr |
2 |
- plots/fdr-control/simulated-bwa.INS.svg
- plots/fdr-control/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| plot_allelefreq |
2 |
- plots/allelefreqs/simulated-bwa.INS.svg
- plots/allelefreqs/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| plot_score_dist |
2 |
- plots/score-dist/simulated-bwa.INS.svg
- plots/score-dist/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| plot_allelefreq_recall |
2 |
- plots/allelefreq-recall/simulated-bwa.INS.svg
- plots/allelefreq-recall/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| plot_allelefreq_scatter |
2 |
- plots/allelefreq-scatter/simulated-bwa.INS.svg
- plots/allelefreq-scatter/simulated-bwa.DEL.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| plot_concordance |
2 |
- plots/concordance/colo1.INS.concordance.svg
- plots/concordance/colo1.DEL.concordance.svg
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| obtain_tp_fp |
416 |
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| aggregate_concordance |
30 |
- aggregated-concordance/varlociraptor-delly-0.9/colo1.INS.tsv
- aggregated-concordance/varlociraptor-lancet-0.9/colo1.INS.tsv
- aggregated-concordance/varlociraptor-manta-0.9/colo1.INS.tsv
- aggregated-concordance/varlociraptor-strelka-0.9/colo1.INS.tsv
- aggregated-concordance/varlociraptor-bpi-0.9/colo1.INS.tsv
- aggregated-concordance/varlociraptor-delly-0.98/colo1.INS.tsv
- aggregated-concordance/varlociraptor-lancet-0.98/colo1.INS.tsv
- aggregated-concordance/varlociraptor-manta-0.98/colo1.INS.tsv
- aggregated-concordance/varlociraptor-strelka-0.98/colo1.INS.tsv
- aggregated-concordance/varlociraptor-bpi-0.98/colo1.INS.tsv
- aggregated-concordance/adhoc-delly-default/colo1.INS.tsv
- aggregated-concordance/adhoc-lancet-default/colo1.INS.tsv
- aggregated-concordance/adhoc-manta-default/colo1.INS.tsv
- aggregated-concordance/adhoc-strelka-default/colo1.INS.tsv
- aggregated-concordance/adhoc-bpi-default/colo1.INS.tsv
- aggregated-concordance/varlociraptor-delly-0.9/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-lancet-0.9/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-manta-0.9/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-strelka-0.9/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-bpi-0.9/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-delly-0.98/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-lancet-0.98/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-manta-0.98/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-strelka-0.98/colo1.DEL.tsv
- aggregated-concordance/varlociraptor-bpi-0.98/colo1.DEL.tsv
- aggregated-concordance/adhoc-delly-default/colo1.DEL.tsv
- aggregated-concordance/adhoc-lancet-default/colo1.DEL.tsv
- aggregated-concordance/adhoc-manta-default/colo1.DEL.tsv
- aggregated-concordance/adhoc-strelka-default/colo1.DEL.tsv
- aggregated-concordance/adhoc-bpi-default/colo1.DEL.tsv
|
|
- python =3.6
- pandas =0.23
- matplotlib =3.0
- seaborn =0.9.0
- pysam =0.13.0
- svgutils =0.2
- pybedtools =0.7.10
- networkx =2.2
|
| varlociraptor_calls_to_tsv |
368 |
|
|
- rust-bio-tools =0.5.0
- bedtools =2.27.1
- bcftools =1.8
|
| other_calls_to_tsv |
8 |
- matched-calls/default-lancet/simulated-bwa.all.tsv
- matched-calls/default-manta/simulated-bwa.all.tsv
- matched-calls/default-strelka/simulated-bwa.all.tsv
- matched-calls/adhoc-delly/simulated-bwa.all.tsv
- matched-calls/adhoc-lancet/simulated-bwa.all.tsv
- matched-calls/adhoc-manta/simulated-bwa.all.tsv
- matched-calls/adhoc-strelka/simulated-bwa.all.tsv
- matched-calls/adhoc-bpi/simulated-bwa.all.tsv
|
|
- rust-bio-tools =0.2.5
- bedtools =2.27.1
- bcftools =1.8
|
| concordance_to_tsv |
60 |
- concordance/varlociraptor-delly-0.9/colo1.0-vs-1.tsv
- concordance/varlociraptor-delly-0.9/colo1.1-vs-2.tsv
- concordance/varlociraptor-delly-0.9/colo1.2-vs-0.tsv
- concordance/varlociraptor-delly-0.9/colo1.2-vs-3.tsv
- concordance/varlociraptor-delly-0.9/colo1.3-vs-0.tsv
- concordance/varlociraptor-delly-0.9/colo1.3-vs-1.tsv
- concordance/varlociraptor-lancet-0.9/colo1.0-vs-1.tsv
- concordance/varlociraptor-lancet-0.9/colo1.1-vs-2.tsv
- concordance/varlociraptor-lancet-0.9/colo1.2-vs-0.tsv
- concordance/varlociraptor-lancet-0.9/colo1.2-vs-3.tsv
- concordance/varlociraptor-lancet-0.9/colo1.3-vs-0.tsv
- concordance/varlociraptor-lancet-0.9/colo1.3-vs-1.tsv
- concordance/varlociraptor-manta-0.9/colo1.0-vs-1.tsv
- concordance/varlociraptor-manta-0.9/colo1.1-vs-2.tsv
- concordance/varlociraptor-manta-0.9/colo1.2-vs-0.tsv
- concordance/varlociraptor-manta-0.9/colo1.2-vs-3.tsv
- concordance/varlociraptor-manta-0.9/colo1.3-vs-0.tsv
- concordance/varlociraptor-manta-0.9/colo1.3-vs-1.tsv
- concordance/varlociraptor-strelka-0.9/colo1.0-vs-1.tsv
- concordance/varlociraptor-strelka-0.9/colo1.1-vs-2.tsv
- concordance/varlociraptor-strelka-0.9/colo1.2-vs-0.tsv
- concordance/varlociraptor-strelka-0.9/colo1.2-vs-3.tsv
- concordance/varlociraptor-strelka-0.9/colo1.3-vs-0.tsv
- concordance/varlociraptor-strelka-0.9/colo1.3-vs-1.tsv
- concordance/varlociraptor-bpi-0.9/colo1.0-vs-1.tsv
- concordance/varlociraptor-bpi-0.9/colo1.1-vs-2.tsv
- concordance/varlociraptor-bpi-0.9/colo1.2-vs-0.tsv
- concordance/varlociraptor-bpi-0.9/colo1.2-vs-3.tsv
- concordance/varlociraptor-bpi-0.9/colo1.3-vs-0.tsv
- concordance/varlociraptor-bpi-0.9/colo1.3-vs-1.tsv
- concordance/varlociraptor-delly-0.98/colo1.0-vs-1.tsv
- concordance/varlociraptor-delly-0.98/colo1.1-vs-2.tsv
- concordance/varlociraptor-delly-0.98/colo1.2-vs-0.tsv
- concordance/varlociraptor-delly-0.98/colo1.2-vs-3.tsv
- concordance/varlociraptor-delly-0.98/colo1.3-vs-0.tsv
- concordance/varlociraptor-delly-0.98/colo1.3-vs-1.tsv
- concordance/varlociraptor-lancet-0.98/colo1.0-vs-1.tsv
- concordance/varlociraptor-lancet-0.98/colo1.1-vs-2.tsv
- concordance/varlociraptor-lancet-0.98/colo1.2-vs-0.tsv
- concordance/varlociraptor-lancet-0.98/colo1.2-vs-3.tsv
- concordance/varlociraptor-lancet-0.98/colo1.3-vs-0.tsv
- concordance/varlociraptor-lancet-0.98/colo1.3-vs-1.tsv
- concordance/varlociraptor-manta-0.98/colo1.0-vs-1.tsv
- concordance/varlociraptor-manta-0.98/colo1.1-vs-2.tsv
- concordance/varlociraptor-manta-0.98/colo1.2-vs-0.tsv
- concordance/varlociraptor-manta-0.98/colo1.2-vs-3.tsv
- concordance/varlociraptor-manta-0.98/colo1.3-vs-0.tsv
- concordance/varlociraptor-manta-0.98/colo1.3-vs-1.tsv
- concordance/varlociraptor-strelka-0.98/colo1.0-vs-1.tsv
- concordance/varlociraptor-strelka-0.98/colo1.1-vs-2.tsv
- concordance/varlociraptor-strelka-0.98/colo1.2-vs-0.tsv
- concordance/varlociraptor-strelka-0.98/colo1.2-vs-3.tsv
- concordance/varlociraptor-strelka-0.98/colo1.3-vs-0.tsv
- concordance/varlociraptor-strelka-0.98/colo1.3-vs-1.tsv
- concordance/varlociraptor-bpi-0.98/colo1.0-vs-1.tsv
- concordance/varlociraptor-bpi-0.98/colo1.1-vs-2.tsv
- concordance/varlociraptor-bpi-0.98/colo1.2-vs-0.tsv
- concordance/varlociraptor-bpi-0.98/colo1.2-vs-3.tsv
- concordance/varlociraptor-bpi-0.98/colo1.3-vs-0.tsv
- concordance/varlociraptor-bpi-0.98/colo1.3-vs-1.tsv
|
|
- rust-bio-tools =0.5.0
- bedtools =2.27.1
- bcftools =1.8
|
| concordance_to_tsv |
30 |
- concordance/adhoc-delly-default/colo1.0-vs-1.tsv
- concordance/adhoc-delly-default/colo1.1-vs-2.tsv
- concordance/adhoc-delly-default/colo1.2-vs-0.tsv
- concordance/adhoc-delly-default/colo1.2-vs-3.tsv
- concordance/adhoc-delly-default/colo1.3-vs-0.tsv
- concordance/adhoc-delly-default/colo1.3-vs-1.tsv
- concordance/adhoc-lancet-default/colo1.0-vs-1.tsv
- concordance/adhoc-lancet-default/colo1.1-vs-2.tsv
- concordance/adhoc-lancet-default/colo1.2-vs-0.tsv
- concordance/adhoc-lancet-default/colo1.2-vs-3.tsv
- concordance/adhoc-lancet-default/colo1.3-vs-0.tsv
- concordance/adhoc-lancet-default/colo1.3-vs-1.tsv
- concordance/adhoc-manta-default/colo1.0-vs-1.tsv
- concordance/adhoc-manta-default/colo1.1-vs-2.tsv
- concordance/adhoc-manta-default/colo1.2-vs-0.tsv
- concordance/adhoc-manta-default/colo1.2-vs-3.tsv
- concordance/adhoc-manta-default/colo1.3-vs-0.tsv
- concordance/adhoc-manta-default/colo1.3-vs-1.tsv
- concordance/adhoc-strelka-default/colo1.0-vs-1.tsv
- concordance/adhoc-strelka-default/colo1.1-vs-2.tsv
- concordance/adhoc-strelka-default/colo1.2-vs-0.tsv
- concordance/adhoc-strelka-default/colo1.2-vs-3.tsv
- concordance/adhoc-strelka-default/colo1.3-vs-0.tsv
- concordance/adhoc-strelka-default/colo1.3-vs-1.tsv
- concordance/adhoc-bpi-default/colo1.0-vs-1.tsv
- concordance/adhoc-bpi-default/colo1.1-vs-2.tsv
- concordance/adhoc-bpi-default/colo1.2-vs-0.tsv
- concordance/adhoc-bpi-default/colo1.2-vs-3.tsv
- concordance/adhoc-bpi-default/colo1.3-vs-0.tsv
- concordance/adhoc-bpi-default/colo1.3-vs-1.tsv
|
|
- rust-bio-tools =0.2.5
- bedtools =2.27.1
- bcftools =1.8
|
| varlociraptor_all_calls_to_tsv |
20 |
- varlociraptor-delly/COLO_829-GSC.all.tsv
- varlociraptor-delly/COLO_829-Ill.all.tsv
- varlociraptor-delly/COLO_829-TGen.all.tsv
- varlociraptor-delly/COLO_829-EBI.all.tsv
- varlociraptor-lancet/COLO_829-GSC.all.tsv
- varlociraptor-lancet/COLO_829-Ill.all.tsv
- varlociraptor-lancet/COLO_829-TGen.all.tsv
- varlociraptor-lancet/COLO_829-EBI.all.tsv
- varlociraptor-manta/COLO_829-GSC.all.tsv
- varlociraptor-manta/COLO_829-Ill.all.tsv
- varlociraptor-manta/COLO_829-TGen.all.tsv
- varlociraptor-manta/COLO_829-EBI.all.tsv
- varlociraptor-strelka/COLO_829-GSC.all.tsv
- varlociraptor-strelka/COLO_829-Ill.all.tsv
- varlociraptor-strelka/COLO_829-TGen.all.tsv
- varlociraptor-strelka/COLO_829-EBI.all.tsv
- varlociraptor-bpi/COLO_829-GSC.all.tsv
- varlociraptor-bpi/COLO_829-Ill.all.tsv
- varlociraptor-bpi/COLO_829-TGen.all.tsv
- varlociraptor-bpi/COLO_829-EBI.all.tsv
|
|
- rust-bio-tools =0.5.0
- bedtools =2.27.1
- bcftools =1.8
|
| match_varlociraptor_calls |
368 |
|
|
- rust-bio-tools =0.5.0
- bedtools =2.27.1
- bcftools =1.8
|
| match_other_calls |
8 |
- matched-calls/default-lancet/simulated-bwa.all.bcf
- matched-calls/default-manta/simulated-bwa.all.bcf
- matched-calls/default-strelka/simulated-bwa.all.bcf
- matched-calls/adhoc-delly/simulated-bwa.all.bcf
- matched-calls/adhoc-lancet/simulated-bwa.all.bcf
- matched-calls/adhoc-manta/simulated-bwa.all.bcf
- matched-calls/adhoc-strelka/simulated-bwa.all.bcf
- matched-calls/adhoc-bpi/simulated-bwa.all.bcf
|
|
|
| concordance_match |
60 |
- concordance/varlociraptor-delly-0.9/colo1.0-vs-1.bcf
- concordance/varlociraptor-delly-0.9/colo1.1-vs-2.bcf
- concordance/varlociraptor-delly-0.9/colo1.2-vs-0.bcf
- concordance/varlociraptor-delly-0.9/colo1.2-vs-3.bcf
- concordance/varlociraptor-delly-0.9/colo1.3-vs-0.bcf
- concordance/varlociraptor-delly-0.9/colo1.3-vs-1.bcf
- concordance/varlociraptor-lancet-0.9/colo1.0-vs-1.bcf
- concordance/varlociraptor-lancet-0.9/colo1.1-vs-2.bcf
- concordance/varlociraptor-lancet-0.9/colo1.2-vs-0.bcf
- concordance/varlociraptor-lancet-0.9/colo1.2-vs-3.bcf
- concordance/varlociraptor-lancet-0.9/colo1.3-vs-0.bcf
- concordance/varlociraptor-lancet-0.9/colo1.3-vs-1.bcf
- concordance/varlociraptor-manta-0.9/colo1.0-vs-1.bcf
- concordance/varlociraptor-manta-0.9/colo1.1-vs-2.bcf
- concordance/varlociraptor-manta-0.9/colo1.2-vs-0.bcf
- concordance/varlociraptor-manta-0.9/colo1.2-vs-3.bcf
- concordance/varlociraptor-manta-0.9/colo1.3-vs-0.bcf
- concordance/varlociraptor-manta-0.9/colo1.3-vs-1.bcf
- concordance/varlociraptor-strelka-0.9/colo1.0-vs-1.bcf
- concordance/varlociraptor-strelka-0.9/colo1.1-vs-2.bcf
- concordance/varlociraptor-strelka-0.9/colo1.2-vs-0.bcf
- concordance/varlociraptor-strelka-0.9/colo1.2-vs-3.bcf
- concordance/varlociraptor-strelka-0.9/colo1.3-vs-0.bcf
- concordance/varlociraptor-strelka-0.9/colo1.3-vs-1.bcf
- concordance/varlociraptor-bpi-0.9/colo1.0-vs-1.bcf
- concordance/varlociraptor-bpi-0.9/colo1.1-vs-2.bcf
- concordance/varlociraptor-bpi-0.9/colo1.2-vs-0.bcf
- concordance/varlociraptor-bpi-0.9/colo1.2-vs-3.bcf
- concordance/varlociraptor-bpi-0.9/colo1.3-vs-0.bcf
- concordance/varlociraptor-bpi-0.9/colo1.3-vs-1.bcf
- concordance/varlociraptor-delly-0.98/colo1.0-vs-1.bcf
- concordance/varlociraptor-delly-0.98/colo1.1-vs-2.bcf
- concordance/varlociraptor-delly-0.98/colo1.2-vs-0.bcf
- concordance/varlociraptor-delly-0.98/colo1.2-vs-3.bcf
- concordance/varlociraptor-delly-0.98/colo1.3-vs-0.bcf
- concordance/varlociraptor-delly-0.98/colo1.3-vs-1.bcf
- concordance/varlociraptor-lancet-0.98/colo1.0-vs-1.bcf
- concordance/varlociraptor-lancet-0.98/colo1.1-vs-2.bcf
- concordance/varlociraptor-lancet-0.98/colo1.2-vs-0.bcf
- concordance/varlociraptor-lancet-0.98/colo1.2-vs-3.bcf
- concordance/varlociraptor-lancet-0.98/colo1.3-vs-0.bcf
- concordance/varlociraptor-lancet-0.98/colo1.3-vs-1.bcf
- concordance/varlociraptor-manta-0.98/colo1.0-vs-1.bcf
- concordance/varlociraptor-manta-0.98/colo1.1-vs-2.bcf
- concordance/varlociraptor-manta-0.98/colo1.2-vs-0.bcf
- concordance/varlociraptor-manta-0.98/colo1.2-vs-3.bcf
- concordance/varlociraptor-manta-0.98/colo1.3-vs-0.bcf
- concordance/varlociraptor-manta-0.98/colo1.3-vs-1.bcf
- concordance/varlociraptor-strelka-0.98/colo1.0-vs-1.bcf
- concordance/varlociraptor-strelka-0.98/colo1.1-vs-2.bcf
- concordance/varlociraptor-strelka-0.98/colo1.2-vs-0.bcf
- concordance/varlociraptor-strelka-0.98/colo1.2-vs-3.bcf
- concordance/varlociraptor-strelka-0.98/colo1.3-vs-0.bcf
- concordance/varlociraptor-strelka-0.98/colo1.3-vs-1.bcf
- concordance/varlociraptor-bpi-0.98/colo1.0-vs-1.bcf
- concordance/varlociraptor-bpi-0.98/colo1.1-vs-2.bcf
- concordance/varlociraptor-bpi-0.98/colo1.2-vs-0.bcf
- concordance/varlociraptor-bpi-0.98/colo1.2-vs-3.bcf
- concordance/varlociraptor-bpi-0.98/colo1.3-vs-0.bcf
- concordance/varlociraptor-bpi-0.98/colo1.3-vs-1.bcf
|
|
- rust-bio-tools =0.5.0
- bedtools =2.27.1
- bcftools =1.8
|
| concordance_match |
30 |
- concordance/adhoc-delly-default/colo1.0-vs-1.bcf
- concordance/adhoc-delly-default/colo1.1-vs-2.bcf
- concordance/adhoc-delly-default/colo1.2-vs-0.bcf
- concordance/adhoc-delly-default/colo1.2-vs-3.bcf
- concordance/adhoc-delly-default/colo1.3-vs-0.bcf
- concordance/adhoc-delly-default/colo1.3-vs-1.bcf
- concordance/adhoc-lancet-default/colo1.0-vs-1.bcf
- concordance/adhoc-lancet-default/colo1.1-vs-2.bcf
- concordance/adhoc-lancet-default/colo1.2-vs-0.bcf
- concordance/adhoc-lancet-default/colo1.2-vs-3.bcf
- concordance/adhoc-lancet-default/colo1.3-vs-0.bcf
- concordance/adhoc-lancet-default/colo1.3-vs-1.bcf
- concordance/adhoc-manta-default/colo1.0-vs-1.bcf
- concordance/adhoc-manta-default/colo1.1-vs-2.bcf
- concordance/adhoc-manta-default/colo1.2-vs-0.bcf
- concordance/adhoc-manta-default/colo1.2-vs-3.bcf
- concordance/adhoc-manta-default/colo1.3-vs-0.bcf
- concordance/adhoc-manta-default/colo1.3-vs-1.bcf
- concordance/adhoc-strelka-default/colo1.0-vs-1.bcf
- concordance/adhoc-strelka-default/colo1.1-vs-2.bcf
- concordance/adhoc-strelka-default/colo1.2-vs-0.bcf
- concordance/adhoc-strelka-default/colo1.2-vs-3.bcf
- concordance/adhoc-strelka-default/colo1.3-vs-0.bcf
- concordance/adhoc-strelka-default/colo1.3-vs-1.bcf
- concordance/adhoc-bpi-default/colo1.0-vs-1.bcf
- concordance/adhoc-bpi-default/colo1.1-vs-2.bcf
- concordance/adhoc-bpi-default/colo1.2-vs-0.bcf
- concordance/adhoc-bpi-default/colo1.2-vs-3.bcf
- concordance/adhoc-bpi-default/colo1.3-vs-0.bcf
- concordance/adhoc-bpi-default/colo1.3-vs-1.bcf
|
|
- rust-bio-tools =0.2.5
- bedtools =2.27.1
- bcftools =1.8
|
| varlociraptor_merge |
24 |
- varlociraptor-delly/COLO_829-GSC.all.bcf
- varlociraptor-delly/COLO_829-Ill.all.bcf
- varlociraptor-delly/COLO_829-TGen.all.bcf
- varlociraptor-delly/COLO_829-EBI.all.bcf
- varlociraptor-lancet/COLO_829-GSC.all.bcf
- varlociraptor-lancet/COLO_829-Ill.all.bcf
- varlociraptor-lancet/COLO_829-TGen.all.bcf
- varlociraptor-lancet/COLO_829-EBI.all.bcf
- varlociraptor-manta/COLO_829-GSC.all.bcf
- varlociraptor-manta/COLO_829-Ill.all.bcf
- varlociraptor-manta/COLO_829-TGen.all.bcf
- varlociraptor-manta/COLO_829-EBI.all.bcf
- varlociraptor-strelka/COLO_829-GSC.all.bcf
- varlociraptor-strelka/COLO_829-Ill.all.bcf
- varlociraptor-strelka/COLO_829-TGen.all.bcf
- varlociraptor-strelka/COLO_829-EBI.all.bcf
- varlociraptor-bpi/COLO_829-GSC.all.bcf
- varlociraptor-bpi/COLO_829-Ill.all.bcf
- varlociraptor-bpi/COLO_829-TGen.all.bcf
- varlociraptor-bpi/COLO_829-EBI.all.bcf
- varlociraptor-delly/simulated-bwa.all.bcf
- varlociraptor-lancet/simulated-bwa.all.bcf
- varlociraptor-manta/simulated-bwa.all.bcf
- varlociraptor-strelka/simulated-bwa.all.bcf
|
|
|
| varlociraptor_control_fdr |
368 |
|
|
|
| adhoc_varlociraptor |
40 |
- varlociraptor-delly/COLO_829-GSC.adhoc.0.9.bcf
- varlociraptor-delly/COLO_829-Ill.adhoc.0.9.bcf
- varlociraptor-delly/COLO_829-TGen.adhoc.0.9.bcf
- varlociraptor-delly/COLO_829-EBI.adhoc.0.9.bcf
- varlociraptor-lancet/COLO_829-GSC.adhoc.0.9.bcf
- varlociraptor-lancet/COLO_829-Ill.adhoc.0.9.bcf
- varlociraptor-lancet/COLO_829-TGen.adhoc.0.9.bcf
- varlociraptor-lancet/COLO_829-EBI.adhoc.0.9.bcf
- varlociraptor-manta/COLO_829-GSC.adhoc.0.9.bcf
- varlociraptor-manta/COLO_829-Ill.adhoc.0.9.bcf
- varlociraptor-manta/COLO_829-TGen.adhoc.0.9.bcf
- varlociraptor-manta/COLO_829-EBI.adhoc.0.9.bcf
- varlociraptor-strelka/COLO_829-GSC.adhoc.0.9.bcf
- varlociraptor-strelka/COLO_829-Ill.adhoc.0.9.bcf
- varlociraptor-strelka/COLO_829-TGen.adhoc.0.9.bcf
- varlociraptor-strelka/COLO_829-EBI.adhoc.0.9.bcf
- varlociraptor-bpi/COLO_829-GSC.adhoc.0.9.bcf
- varlociraptor-bpi/COLO_829-Ill.adhoc.0.9.bcf
- varlociraptor-bpi/COLO_829-TGen.adhoc.0.9.bcf
- varlociraptor-bpi/COLO_829-EBI.adhoc.0.9.bcf
- varlociraptor-delly/COLO_829-GSC.adhoc.0.98.bcf
- varlociraptor-delly/COLO_829-Ill.adhoc.0.98.bcf
- varlociraptor-delly/COLO_829-TGen.adhoc.0.98.bcf
- varlociraptor-delly/COLO_829-EBI.adhoc.0.98.bcf
- varlociraptor-lancet/COLO_829-GSC.adhoc.0.98.bcf
- varlociraptor-lancet/COLO_829-Ill.adhoc.0.98.bcf
- varlociraptor-lancet/COLO_829-TGen.adhoc.0.98.bcf
- varlociraptor-lancet/COLO_829-EBI.adhoc.0.98.bcf
- varlociraptor-manta/COLO_829-GSC.adhoc.0.98.bcf
- varlociraptor-manta/COLO_829-Ill.adhoc.0.98.bcf
- varlociraptor-manta/COLO_829-TGen.adhoc.0.98.bcf
- varlociraptor-manta/COLO_829-EBI.adhoc.0.98.bcf
- varlociraptor-strelka/COLO_829-GSC.adhoc.0.98.bcf
- varlociraptor-strelka/COLO_829-Ill.adhoc.0.98.bcf
- varlociraptor-strelka/COLO_829-TGen.adhoc.0.98.bcf
- varlociraptor-strelka/COLO_829-EBI.adhoc.0.98.bcf
- varlociraptor-bpi/COLO_829-GSC.adhoc.0.98.bcf
- varlociraptor-bpi/COLO_829-Ill.adhoc.0.98.bcf
- varlociraptor-bpi/COLO_829-TGen.adhoc.0.98.bcf
- varlociraptor-bpi/COLO_829-EBI.adhoc.0.98.bcf
|
|
|
| varlociraptor_call |
600 |
|
|
|
| delly_adhoc |
4 |
- adhoc-delly/COLO_829-GSC.all.bcf
- adhoc-delly/COLO_829-Ill.all.bcf
- adhoc-delly/COLO_829-TGen.all.bcf
- adhoc-delly/COLO_829-EBI.all.bcf
|
|
- delly =0.7.7
- bcftools =1.6
|
| lancet_adhoc |
4 |
- adhoc-lancet/COLO_829-GSC.all.bcf
- adhoc-lancet/COLO_829-Ill.all.bcf
- adhoc-lancet/COLO_829-TGen.all.bcf
- adhoc-lancet/COLO_829-EBI.all.bcf
|
|
|
| manta_adhoc |
4 |
- adhoc-manta/COLO_829-GSC.all.bcf
- adhoc-manta/COLO_829-Ill.all.bcf
- adhoc-manta/COLO_829-TGen.all.bcf
- adhoc-manta/COLO_829-EBI.all.bcf
|
|
|
| strelka_adhoc |
4 |
- adhoc-strelka/COLO_829-GSC.all.bcf
- adhoc-strelka/COLO_829-Ill.all.bcf
- adhoc-strelka/COLO_829-TGen.all.bcf
- adhoc-strelka/COLO_829-EBI.all.bcf
|
|
|
| bpi_adhoc |
4 |
- adhoc-bpi/COLO_829-GSC.all.bcf
- adhoc-bpi/COLO_829-Ill.all.bcf
- adhoc-bpi/COLO_829-TGen.all.bcf
- adhoc-bpi/COLO_829-EBI.all.bcf
|
|
|
| delly_concat |
4 |
- delly/COLO_829-GSC.all.bcf
- delly/COLO_829-Ill.all.bcf
- delly/COLO_829-TGen.all.bcf
- delly/COLO_829-EBI.all.bcf
|
|
|
| index_bcf |
20 |
- delly/COLO_829-GSC.all.bcf.csi
- delly/COLO_829-Ill.all.bcf.csi
- delly/COLO_829-TGen.all.bcf.csi
- delly/COLO_829-EBI.all.bcf.csi
- default-lancet/COLO_829-GSC.all.bcf.csi
- default-lancet/COLO_829-Ill.all.bcf.csi
- default-lancet/COLO_829-TGen.all.bcf.csi
- default-lancet/COLO_829-EBI.all.bcf.csi
- manta/COLO_829-GSC.all.bcf.csi
- manta/COLO_829-Ill.all.bcf.csi
- manta/COLO_829-TGen.all.bcf.csi
- manta/COLO_829-EBI.all.bcf.csi
- default-strelka/COLO_829-GSC.all.bcf.csi
- default-strelka/COLO_829-Ill.all.bcf.csi
- default-strelka/COLO_829-TGen.all.bcf.csi
- default-strelka/COLO_829-EBI.all.bcf.csi
- bpi/COLO_829-GSC.all.bcf.csi
- bpi/COLO_829-Ill.all.bcf.csi
- bpi/COLO_829-TGen.all.bcf.csi
- bpi/COLO_829-EBI.all.bcf.csi
|
|
- bcftools =1.6
- samtools =1.6
|
| mark_duplicates |
8 |
- mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.bam
- mapped-bwa/COLO_829-GSC.tumor.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-GSC.normal.hg38.sorted.bam
- mapped-bwa/COLO_829-GSC.normal.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.bam
- mapped-bwa/COLO_829-Ill.tumor.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-Ill.normal.hg38.sorted.bam
- mapped-bwa/COLO_829-Ill.normal.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.bam
- mapped-bwa/COLO_829-TGen.tumor.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-TGen.normal.hg38.sorted.bam
- mapped-bwa/COLO_829-TGen.normal.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.bam
- mapped-bwa/COLO_829-EBI.tumor.hg38.markdup.metrics.txt
- mapped-bwa/COLO_829-EBI.normal.hg38.sorted.bam
- mapped-bwa/COLO_829-EBI.normal.hg38.markdup.metrics.txt
|
|
|
| samtools_index |
8 |
- mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-GSC.normal.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-Ill.normal.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-TGen.normal.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.bam.bai
- mapped-bwa/COLO_829-EBI.normal.hg38.sorted.bam.bai
|
|
|
| merge_lancet |
4 |
- default-lancet/COLO_829-GSC.all.bcf
- default-lancet/COLO_829-Ill.all.bcf
- default-lancet/COLO_829-TGen.all.bcf
- default-lancet/COLO_829-EBI.all.bcf
|
|
- bcftools =1.6
- samtools =1.6
|
| manta_raw |
4 |
- manta/COLO_829-GSC.all.bcf
- manta/COLO_829-Ill.all.bcf
- manta/COLO_829-TGen.all.bcf
- manta/COLO_829-EBI.all.bcf
|
|
|
| strelka_default |
4 |
- default-strelka/COLO_829-GSC.all.bcf
- default-strelka/COLO_829-Ill.all.bcf
- default-strelka/COLO_829-TGen.all.bcf
- default-strelka/COLO_829-EBI.all.bcf
|
|
|
| bpi_convert |
4 |
- bpi/COLO_829-GSC.all.bcf
- bpi/COLO_829-Ill.all.bcf
- bpi/COLO_829-TGen.all.bcf
- bpi/COLO_829-EBI.all.bcf
|
|
|
| manta_default |
4 |
- default-manta/COLO_829-GSC.all.bcf
- default-manta/COLO_829-Ill.all.bcf
- default-manta/COLO_829-TGen.all.bcf
- default-manta/COLO_829-EBI.all.bcf
|
|
|
| delly |
8 |
- delly/COLO_829-GSC.DEL.bcf
- delly/COLO_829-GSC.INS.bcf
- delly/COLO_829-Ill.DEL.bcf
- delly/COLO_829-Ill.INS.bcf
- delly/COLO_829-TGen.DEL.bcf
- delly/COLO_829-TGen.INS.bcf
- delly/COLO_829-EBI.DEL.bcf
- delly/COLO_829-EBI.INS.bcf
|
|
|
| samtools_sort |
8 |
- mapped-bwa/COLO_829-GSC.tumor.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-GSC.normal.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-Ill.tumor.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-Ill.normal.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-TGen.tumor.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-TGen.normal.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-EBI.tumor.hg38.sorted.pre.bam
- mapped-bwa/COLO_829-EBI.normal.hg38.sorted.pre.bam
|
|
|
| fix_lancet |
100 |
- lancet/COLO_829-GSC/chr1.fixed.vcf
- lancet/COLO_829-GSC/chr2.fixed.vcf
- lancet/COLO_829-GSC/chr3.fixed.vcf
- lancet/COLO_829-GSC/chr4.fixed.vcf
- lancet/COLO_829-GSC/chr5.fixed.vcf
- lancet/COLO_829-GSC/chr6.fixed.vcf
- lancet/COLO_829-GSC/chr7.fixed.vcf
- lancet/COLO_829-GSC/chr8.fixed.vcf
- lancet/COLO_829-GSC/chr9.fixed.vcf
- lancet/COLO_829-GSC/chr10.fixed.vcf
- lancet/COLO_829-GSC/chr11.fixed.vcf
- lancet/COLO_829-GSC/chr12.fixed.vcf
- lancet/COLO_829-GSC/chr13.fixed.vcf
- lancet/COLO_829-GSC/chr14.fixed.vcf
- lancet/COLO_829-GSC/chr15.fixed.vcf
- lancet/COLO_829-GSC/chr16.fixed.vcf
- lancet/COLO_829-GSC/chr17.fixed.vcf
- lancet/COLO_829-GSC/chr18.fixed.vcf
- lancet/COLO_829-GSC/chr19.fixed.vcf
- lancet/COLO_829-GSC/chr20.fixed.vcf
- lancet/COLO_829-GSC/chr21.fixed.vcf
- lancet/COLO_829-GSC/chr22.fixed.vcf
- lancet/COLO_829-GSC/chrM.fixed.vcf
- lancet/COLO_829-GSC/chrX.fixed.vcf
- lancet/COLO_829-GSC/chrY.fixed.vcf
- lancet/COLO_829-Ill/chr1.fixed.vcf
- lancet/COLO_829-Ill/chr2.fixed.vcf
- lancet/COLO_829-Ill/chr3.fixed.vcf
- lancet/COLO_829-Ill/chr4.fixed.vcf
- lancet/COLO_829-Ill/chr5.fixed.vcf
- lancet/COLO_829-Ill/chr6.fixed.vcf
- lancet/COLO_829-Ill/chr7.fixed.vcf
- lancet/COLO_829-Ill/chr8.fixed.vcf
- lancet/COLO_829-Ill/chr9.fixed.vcf
- lancet/COLO_829-Ill/chr10.fixed.vcf
- lancet/COLO_829-Ill/chr11.fixed.vcf
- lancet/COLO_829-Ill/chr12.fixed.vcf
- lancet/COLO_829-Ill/chr13.fixed.vcf
- lancet/COLO_829-Ill/chr14.fixed.vcf
- lancet/COLO_829-Ill/chr15.fixed.vcf
- lancet/COLO_829-Ill/chr16.fixed.vcf
- lancet/COLO_829-Ill/chr17.fixed.vcf
- lancet/COLO_829-Ill/chr18.fixed.vcf
- lancet/COLO_829-Ill/chr19.fixed.vcf
- lancet/COLO_829-Ill/chr20.fixed.vcf
- lancet/COLO_829-Ill/chr21.fixed.vcf
- lancet/COLO_829-Ill/chr22.fixed.vcf
- lancet/COLO_829-Ill/chrM.fixed.vcf
- lancet/COLO_829-Ill/chrX.fixed.vcf
- lancet/COLO_829-Ill/chrY.fixed.vcf
- lancet/COLO_829-TGen/chr1.fixed.vcf
- lancet/COLO_829-TGen/chr2.fixed.vcf
- lancet/COLO_829-TGen/chr3.fixed.vcf
- lancet/COLO_829-TGen/chr4.fixed.vcf
- lancet/COLO_829-TGen/chr5.fixed.vcf
- lancet/COLO_829-TGen/chr6.fixed.vcf
- lancet/COLO_829-TGen/chr7.fixed.vcf
- lancet/COLO_829-TGen/chr8.fixed.vcf
- lancet/COLO_829-TGen/chr9.fixed.vcf
- lancet/COLO_829-TGen/chr10.fixed.vcf
- lancet/COLO_829-TGen/chr11.fixed.vcf
- lancet/COLO_829-TGen/chr12.fixed.vcf
- lancet/COLO_829-TGen/chr13.fixed.vcf
- lancet/COLO_829-TGen/chr14.fixed.vcf
- lancet/COLO_829-TGen/chr15.fixed.vcf
- lancet/COLO_829-TGen/chr16.fixed.vcf
- lancet/COLO_829-TGen/chr17.fixed.vcf
- lancet/COLO_829-TGen/chr18.fixed.vcf
- lancet/COLO_829-TGen/chr19.fixed.vcf
- lancet/COLO_829-TGen/chr20.fixed.vcf
- lancet/COLO_829-TGen/chr21.fixed.vcf
- lancet/COLO_829-TGen/chr22.fixed.vcf
- lancet/COLO_829-TGen/chrM.fixed.vcf
- lancet/COLO_829-TGen/chrX.fixed.vcf
- lancet/COLO_829-TGen/chrY.fixed.vcf
- lancet/COLO_829-EBI/chr1.fixed.vcf
- lancet/COLO_829-EBI/chr2.fixed.vcf
- lancet/COLO_829-EBI/chr3.fixed.vcf
- lancet/COLO_829-EBI/chr4.fixed.vcf
- lancet/COLO_829-EBI/chr5.fixed.vcf
- lancet/COLO_829-EBI/chr6.fixed.vcf
- lancet/COLO_829-EBI/chr7.fixed.vcf
- lancet/COLO_829-EBI/chr8.fixed.vcf
- lancet/COLO_829-EBI/chr9.fixed.vcf
- lancet/COLO_829-EBI/chr10.fixed.vcf
- lancet/COLO_829-EBI/chr11.fixed.vcf
- lancet/COLO_829-EBI/chr12.fixed.vcf
- lancet/COLO_829-EBI/chr13.fixed.vcf
- lancet/COLO_829-EBI/chr14.fixed.vcf
- lancet/COLO_829-EBI/chr15.fixed.vcf
- lancet/COLO_829-EBI/chr16.fixed.vcf
- lancet/COLO_829-EBI/chr17.fixed.vcf
- lancet/COLO_829-EBI/chr18.fixed.vcf
- lancet/COLO_829-EBI/chr19.fixed.vcf
- lancet/COLO_829-EBI/chr20.fixed.vcf
- lancet/COLO_829-EBI/chr21.fixed.vcf
- lancet/COLO_829-EBI/chr22.fixed.vcf
- lancet/COLO_829-EBI/chrM.fixed.vcf
- lancet/COLO_829-EBI/chrX.fixed.vcf
- lancet/COLO_829-EBI/chrY.fixed.vcf
|
|
- bcftools =1.6
- samtools =1.6
|
| manta |
4 |
- manta/COLO_829-GSC/results/variants/candidateSV.vcf.gz
- manta/COLO_829-GSC/results/variants/somaticSV.vcf.gz
- manta/COLO_829-GSC/results/variants/candidateSmallIndels.vcf.gz
- manta/COLO_829-Ill/results/variants/candidateSV.vcf.gz
- manta/COLO_829-Ill/results/variants/somaticSV.vcf.gz
- manta/COLO_829-Ill/results/variants/candidateSmallIndels.vcf.gz
- manta/COLO_829-TGen/results/variants/candidateSV.vcf.gz
- manta/COLO_829-TGen/results/variants/somaticSV.vcf.gz
- manta/COLO_829-TGen/results/variants/candidateSmallIndels.vcf.gz
- manta/COLO_829-EBI/results/variants/candidateSV.vcf.gz
- manta/COLO_829-EBI/results/variants/somaticSV.vcf.gz
- manta/COLO_829-EBI/results/variants/candidateSmallIndels.vcf.gz
|
|
|
| strelka |
4 |
- strelka/COLO_829-GSC/results/variants/somatic.snvs.vcf.gz
- strelka/COLO_829-GSC/results/variants/somatic.indels.vcf.gz
- strelka/COLO_829-Ill/results/variants/somatic.snvs.vcf.gz
- strelka/COLO_829-Ill/results/variants/somatic.indels.vcf.gz
- strelka/COLO_829-TGen/results/variants/somatic.snvs.vcf.gz
- strelka/COLO_829-TGen/results/variants/somatic.indels.vcf.gz
- strelka/COLO_829-EBI/results/variants/somatic.snvs.vcf.gz
- strelka/COLO_829-EBI/results/variants/somatic.indels.vcf.gz
|
|
|
| bpi |
4 |
- bpi/COLO_829-GSC.all.vcf
- bpi/COLO_829-Ill.all.vcf
- bpi/COLO_829-TGen.all.vcf
- bpi/COLO_829-EBI.all.vcf
|
|
- break-point-inspector =1.5
|
| bwa |
8 |
- mapped-bwa/COLO_829-GSC.tumor.hg38.bam
- mapped-bwa/COLO_829-GSC.normal.hg38.bam
- mapped-bwa/COLO_829-Ill.tumor.hg38.bam
- mapped-bwa/COLO_829-Ill.normal.hg38.bam
- mapped-bwa/COLO_829-TGen.tumor.hg38.bam
- mapped-bwa/COLO_829-TGen.normal.hg38.bam
- mapped-bwa/COLO_829-EBI.tumor.hg38.bam
- mapped-bwa/COLO_829-EBI.normal.hg38.bam
|
|
- python
- samtools =1.6
- numpy
- scikit-learn
- pandas
- setuptools
|
| lancet |
75 |
- lancet/COLO_829-GSC/chr1.vcf
- lancet/COLO_829-GSC/chr2.vcf
- lancet/COLO_829-GSC/chr3.vcf
- lancet/COLO_829-GSC/chr4.vcf
- lancet/COLO_829-GSC/chr5.vcf
- lancet/COLO_829-GSC/chr6.vcf
- lancet/COLO_829-GSC/chr7.vcf
- lancet/COLO_829-GSC/chr8.vcf
- lancet/COLO_829-GSC/chr9.vcf
- lancet/COLO_829-GSC/chr10.vcf
- lancet/COLO_829-GSC/chr11.vcf
- lancet/COLO_829-GSC/chr12.vcf
- lancet/COLO_829-GSC/chr13.vcf
- lancet/COLO_829-GSC/chr14.vcf
- lancet/COLO_829-GSC/chr15.vcf
- lancet/COLO_829-GSC/chr16.vcf
- lancet/COLO_829-GSC/chr17.vcf
- lancet/COLO_829-GSC/chr18.vcf
- lancet/COLO_829-GSC/chr19.vcf
- lancet/COLO_829-GSC/chr20.vcf
- lancet/COLO_829-GSC/chr21.vcf
- lancet/COLO_829-GSC/chr22.vcf
- lancet/COLO_829-GSC/chrM.vcf
- lancet/COLO_829-GSC/chrX.vcf
- lancet/COLO_829-GSC/chrY.vcf
- lancet/COLO_829-Ill/chr1.vcf
- lancet/COLO_829-Ill/chr2.vcf
- lancet/COLO_829-Ill/chr3.vcf
- lancet/COLO_829-Ill/chr4.vcf
- lancet/COLO_829-Ill/chr5.vcf
- lancet/COLO_829-Ill/chr6.vcf
- lancet/COLO_829-Ill/chr7.vcf
- lancet/COLO_829-Ill/chr8.vcf
- lancet/COLO_829-Ill/chr9.vcf
- lancet/COLO_829-Ill/chr10.vcf
- lancet/COLO_829-Ill/chr11.vcf
- lancet/COLO_829-Ill/chr12.vcf
- lancet/COLO_829-Ill/chr13.vcf
- lancet/COLO_829-Ill/chr14.vcf
- lancet/COLO_829-Ill/chr15.vcf
- lancet/COLO_829-Ill/chr16.vcf
- lancet/COLO_829-Ill/chr17.vcf
- lancet/COLO_829-Ill/chr18.vcf
- lancet/COLO_829-Ill/chr19.vcf
- lancet/COLO_829-Ill/chr20.vcf
- lancet/COLO_829-Ill/chr21.vcf
- lancet/COLO_829-Ill/chr22.vcf
- lancet/COLO_829-Ill/chrM.vcf
- lancet/COLO_829-Ill/chrX.vcf
- lancet/COLO_829-Ill/chrY.vcf
- lancet/COLO_829-TGen/chr1.vcf
- lancet/COLO_829-TGen/chr2.vcf
- lancet/COLO_829-TGen/chr3.vcf
- lancet/COLO_829-TGen/chr4.vcf
- lancet/COLO_829-TGen/chr5.vcf
- lancet/COLO_829-TGen/chr6.vcf
- lancet/COLO_829-TGen/chr7.vcf
- lancet/COLO_829-TGen/chr8.vcf
- lancet/COLO_829-TGen/chr9.vcf
- lancet/COLO_829-TGen/chr10.vcf
- lancet/COLO_829-TGen/chr11.vcf
- lancet/COLO_829-TGen/chr12.vcf
- lancet/COLO_829-TGen/chr13.vcf
- lancet/COLO_829-TGen/chr14.vcf
- lancet/COLO_829-TGen/chr15.vcf
- lancet/COLO_829-TGen/chr16.vcf
- lancet/COLO_829-TGen/chr17.vcf
- lancet/COLO_829-TGen/chr18.vcf
- lancet/COLO_829-TGen/chr19.vcf
- lancet/COLO_829-TGen/chr20.vcf
- lancet/COLO_829-TGen/chr21.vcf
- lancet/COLO_829-TGen/chr22.vcf
- lancet/COLO_829-TGen/chrM.vcf
- lancet/COLO_829-TGen/chrX.vcf
- lancet/COLO_829-TGen/chrY.vcf
|
|
|
| lancet |
25 |
- lancet/COLO_829-EBI/chr1.vcf
- lancet/COLO_829-EBI/chr2.vcf
- lancet/COLO_829-EBI/chr3.vcf
- lancet/COLO_829-EBI/chr4.vcf
- lancet/COLO_829-EBI/chr5.vcf
- lancet/COLO_829-EBI/chr6.vcf
- lancet/COLO_829-EBI/chr7.vcf
- lancet/COLO_829-EBI/chr8.vcf
- lancet/COLO_829-EBI/chr9.vcf
- lancet/COLO_829-EBI/chr10.vcf
- lancet/COLO_829-EBI/chr11.vcf
- lancet/COLO_829-EBI/chr12.vcf
- lancet/COLO_829-EBI/chr13.vcf
- lancet/COLO_829-EBI/chr14.vcf
- lancet/COLO_829-EBI/chr15.vcf
- lancet/COLO_829-EBI/chr16.vcf
- lancet/COLO_829-EBI/chr17.vcf
- lancet/COLO_829-EBI/chr18.vcf
- lancet/COLO_829-EBI/chr19.vcf
- lancet/COLO_829-EBI/chr20.vcf
- lancet/COLO_829-EBI/chr21.vcf
- lancet/COLO_829-EBI/chr22.vcf
- lancet/COLO_829-EBI/chrM.vcf
- lancet/COLO_829-EBI/chrX.vcf
- lancet/COLO_829-EBI/chrY.vcf
|
|
|
| bam2fq |
4 |
- reads/COLO_829-Ill.tumor.1.fastq.gz
- reads/COLO_829-Ill.tumor.2.fastq.gz
- reads/COLO_829-Ill.tumor.fastq.gz
- reads/COLO_829-Ill.normal.1.fastq.gz
- reads/COLO_829-Ill.normal.2.fastq.gz
- reads/COLO_829-Ill.normal.fastq.gz
- reads/COLO_829-TGen.tumor.1.fastq.gz
- reads/COLO_829-TGen.tumor.2.fastq.gz
- reads/COLO_829-TGen.tumor.fastq.gz
- reads/COLO_829-TGen.normal.1.fastq.gz
- reads/COLO_829-TGen.normal.2.fastq.gz
- reads/COLO_829-TGen.normal.fastq.gz
|
|
- bcftools =1.6
- samtools =1.6
|
| prepare_bam |
8 |
- reads/COLO_829-GSC.tumor.namesorted.bam
- reads/COLO_829-GSC.normal.namesorted.bam
- reads/COLO_829-Ill.tumor.namesorted.bam
- reads/COLO_829-Ill.normal.namesorted.bam
- reads/COLO_829-TGen.tumor.namesorted.bam
- reads/COLO_829-TGen.normal.namesorted.bam
- reads/COLO_829-EBI.tumor.namesorted.bam
- reads/COLO_829-EBI.normal.namesorted.bam
|
|
|